A novel role of metal response element binding transcription factor 2 at the Hox gene cluster in the regulation of H3K27me3 by polycomb repressive complex 2

Polycomb repressive complex 2 (PRC2) is known to play an important role in the regulation of early embryonic development, differentiation, and cellular proliferation by introducing methyl groups onto lysine 27 of histone H3 (H3K27me3). PRC2 is tightly associated with silencing of Hox gene clusters and their sequential activation, leading to normal development and differentiation. To investigate epigenetic changes induced by PRC2 during differentiation, deposition of PRC2 components and levels of H3K27me3 were extensively examined using mouse F9 cells as a model system. Contrary to positive correlation between PRC2 deposition and H3K27me3 level, down-regulation of PRC2 components by shRNA and inhibition of EZH1/2 resulted in unexpected elevation of H3K27me3 level at the Hox gene cluster despite its global decrease. We found that metal response element binding transcriptional factor 2 (MTF2), one of sub-stoichiometric components of PRC2, was stably bound to Hox genes. Its binding capability was dependent on other core PRC2 components. A high level of H3K27me3 at Hox genes in Suz12-knock out cells was reversed by knockdown of Mtf2.This shows that MTF2 is necessary to consolidate PRC2-mediated histone methylation. Taken together, our results indicate that expression of Hox gene clusters during differentiation is strictly modulated by the activity of PRC2 secured by MTF2.11Yscopu

ZNF224, Krüppel like zinc finger protein, induces cell growth and apoptosis-resistance by down-regulation of p21 and p53 via miR-663a

ZNF224 is a Kruppel-associated box-containing zinc-finger protein which represses gene transcription by interacting with various co-repressors. However, its consensus DNA sequences and target genes are not fully identified. In this study, we identified and characterized consensus DNA sequences containing 5'-CAGC-3' recognized by ZNF224 through ChIP-sequencing, which further confirmed by ELISA, SPR, qPCR, and luciferase activity assay. ZNF224 increased miR-663a transcription by binding to miR-663a promoter, which in turn binds to 3' UTR of p53 and p21 to decrease their expression. miR-663a antagonist abolished ZNF224-mediated suppression of p21 and p53, resulting in the enhanced apoptosis by CPT. The analyses using human breast ductal carcinoma tissues exhibited that the expression of ZNF224 and miR-663a was increased in cancer compared to non-cancer region. Consequently, ZNF224 increases cell survival and decreases apoptosis by decreasing the expression of p53 and p21 via miR-663a as a transcriptional activator. Taken together, we identified and characterized DNA binding element of ZNF224, and its target genes, miR-663a, which provides a novel insight in the down-regulation of p21 and p53 via miR-663a by ZNF224 in breast cancer.1112Ysciescopu

Identification of the early and late responder genes during the generation of induced pluripotent stem cells from mouse fibroblasts

111Ysciescopu

Prefoldin 6 mediates longevity response from heat shock factor 1 to FOXO in C-elegans

Heat shock factor 1 (HSF-1) and forkhead box O (FOXO) are key transcription factors that protect cells from various stresses. In Caenorhabditis elegans, HSF-1 and FOXO together promote a long life span when insulin/IGF-1 signaling (IIS) is reduced. However, it remains poorly understood how HSF-1 and FOXO cooperate to confer IIS-mediated longevity. Here, we show that prefoldin 6 (PFD-6), a component of the molecular chaperone prefoldin-like complex, relays longevity response from HSF-1 to FOXO under reduced IIS. We found that PFD-6 was specifically required for reduced IIS-mediated longevity by acting in the intestine and hypodermis. We showed that HSF-1 increased the levels of PFD-6 proteins, which in turn directly bound FOXO and enhanced its transcriptional activity. Our work suggests that the prefoldin-like chaperone complex mediates longevity response from HSF-1 to FOXO to increase the life span in animals with reduced IIS.11Ysciescopu

CD82/KAI1 Maintains the Dormancy of Long-Term Hematopoietic Stem Cells through Interaction with DARC- Expressing Macrophages

Hematopoiesis is regulated by crosstalk between long-term repopulating hematopoietic stem cells (LT-HSCs) and supporting niche cells in the bone marrow (BM). Here, we examine the role of CD82/ KAI1 in niche-mediated LT-HSC maintenance. We found that CD82/ KAI1 is expressed predominantly on LT-HSCs and rarely on other hematopoietic stem-progenitor cells (HSPCs). In Cd82 +/-/+/- mice, LTHSCs were selectively lost as they exited from quiescence and differentiated. Mechanistically, CD82based TGF-b1/ Smad3 signaling leads to induction of CDK inhibitors and cell-cycle inhibition. The CD82 binding partner DARC/ CD234 is expressed on macrophages and stabilizes CD82 on LT-HSCs, promoting their quiescence. When DARC + BMmacrophages were ablated, the level of surface CD82 on LT-HSCs decreased, leading to cell-cycle entry, proliferation, and differentiation. A similar interaction appears to be relevant for human HSPCs. Thus, CD82 is a functional surface marker of LT-HSCs that maintains quiescence through interaction with DARC-expressing macrophages in the BM stem cell niche.113525Ysciescopu

Bioinformatics services for analyzing massive genomic datasets

The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and ensuing computational problems. In Korea, the amount of genomic data has been increasing rapidly in the recent years. Leveraging these big data requires researchers to use large-scale computational resources and analysis pipelines. A promising solution for addressing this computational challenge is cloud computing, where CPUs, memory, storage, and programs are accessible in the form of virtual machines. Here, we present a cloud computing-based system, Bio-Express, that provides user-friendly, cost-effective analysis of massive genomic datasets. Bio-Express is loaded with predefined multi-omics data analysis pipelines, which are divided into genome, transcriptome, epigenome, and metagenome pipelines. Users can employ predefined pipelines or create a new pipeline for analyzing their own omics data. We also developed several web-based services for facilitating down-stream analysis of genome data. Bio-Express web service is freely available at https://www. bioexpress.re.kr/. ?? 2020, Korea Genome Organization

A Follow-up Association Study of Genetic Variants for Bone Mineral Density in a Korean Population

국내22kciothe

Comparison of multiple ChIP-Seq peak calling programs for the optimal histone modification profiling

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Orthologous grouping and comparison of prokaryotic and eukaryotic EV proteomes

Introduction: Most prokaryotic and eukaryotic cells secrete Extracellular vesicles (EVs) with bioactive molecules, including proteins and nucleic acid. Protein cargos important for EV biogenesis and/or biological functions can be found using proteomic analyses. Methods: To analyze the similarity and difference between prokaryotic and eukaryotic EVs, EV protein databases was obtained from EVPedia (http://evpedia.info), regardless of EV sources and analysing platforms. EV proteins were catalogued into orthologous groups and annotated these groups using eggNOG database. Gene set enrichment analysis (GSEA) was employed to determine how much the orthologous groups are enriched in EVs of prokaryotic or eukaryotic species. The core network of prokaryotic and eukaryotic EV orthologous groups were explored by Generalized HotNet analysis. Only hot clusters with more than four orthologous groups were visualized by Cytoscape. Results: A total of 6,634 proteomic orthologous groups were identified from 33 prokaryotes and 22 and separated into two distinct groups. Each orthologous group was annotated with gene symbols, GO terms, as well as functional interactions. Frequently detected orthologous groups were related with mainly membrane-associated compartments. The GSEA analysis showed some common and specific proteins to prokaryote or eukaryote in the categories of biological process and cellular component. The correlation network analysis clearly provided a domain-specific terms such as intracellular organelle cilium, cytoplasm ribosome, and ribosome proteasome complex for eukaryotes, and cytoplasm envelope, extracellular exosome, and cell outer membrane for prokayrotes. Summary/Conclusion: Our comprehensive EV proteome analysis could provide a functional modules related with characteristic biological mechanisms in prokayrotes and eukaryotes. This analytical strategy will also provide a new integrative method to investigate EV proteins and propose an evolutionary protein repertoire of EV.1

Chromatin structural changes during intestinal organoid generation from mouse embryonic stem cells

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